presentation.qmd

Group 24

Analysis of Biological Factors affecting pediatric Patients subjected to Unmanipulated Allogeneic unrelated donor Hematopoietic Stem Cell Transplantation

Group 24: Christian, Helena, Lanjing, Inma and Pernille


Aim: The goal of the project is to analyze which biological factors affect the patient survival rate after the transplantation

Slide 2 - Why did we use R?

Topic:

  • A bone marrow transplant is the replacement of damaged blood cells for healthy stems cells
  • The success of the transplantion can depend on many different biological factors
  • These factors influences the recovery of the immune system after the transplantion

Methodology:

R programming language is a powerful tool that allowed us to clean, visualize, organize, and manipulate the data. Therefore, we were able to understand the correlation of the different varibales affecting to the survival rate after the transplant.

Data Wrangling

Dataset: Bone marrow transplant: Children (Donated 20/04/2020)

File: bone-marrow.ariff

An Attribute-Relation File format, .ariff

Content: two destinct sections: Header & Data

With comments using: “%”

Header Data

  • Contains Metadata

  • Name of Relation

  • List of Attributes

  • Contains Data information

  • comma seperated entries

Steps:

  1. Download file into newly created data folders
  2. Extract metadata & data into two files: a .txt and a .tsv containing tidy data: metadata.txt.gz & data.tsv.gz
  3. Augment columns & binary values

Description of the data

Table 1. Information on the subjects included in the data.

Parameter ALL AML chronic lymphoma nonmalignant
N 67 33 45 9 32
Male patients 41 (61.2 %) 17 (51.5 %) 25 (55.6 %) 7 (77.8 %) 21 (65.6 %)
Median recipient age 8 14 11 13 8
Relapse 12 (17.9 %) 5 (15.2 %) 6 (13.3 %) 4 (44.4 %) 1 (3.1 %)
Deceased patients 30 (44.8 %) 15 (45.5 %) 19 (42.2 %) 9 (100 %) 12 (37.5 %)
Median follow-up time for survived patients (days) 1301 1561 1867 NA 1327
Median survival time for deceased patients (days) 168 274 130 67 130


  • ALL, AML, chronic and non-malignant: large patient cohort

  • Lymphoma patients: small patient cohort (careful interpretation needed)

  • A majority was male among all diseases

  • Median recipient age did not vary greatly among diseases, but included both pre-adolescent and adolescent ages

  • A minority (<18 %) experienced relapse, except in the lymphoma group (almost half)

  • A majority survived, except for lymphoma patients

  • Median follow-up time for surviving patients were around 3.5 to 6 years depending on the disease

  • Median survival time for deceased patients varied from around 2 (lymphoma) to around 9 (AML) months

PCA analysis

Include: (Exploratory Analysis, PCA)

Slide 6

Include:

Recipientage, Disease type, Rbodymass index VS Survival rate

The boxplot plot compares the age distribution of the recipients among the different diseases types, while dividing them by their survival status: alive and dead.

Relevant outcomes:

  • Patients with lymphoma had a survial rate of 0%.

  • Age might be associated with mortality, since older patients have higher mortality than young ones.

  • Every disease type exhibited higher mortality than survival.

The bar plot reveals the relationship between the BMI with survival rate. It showed that survival decreases while BMI increases. Underweight patients had the highest amount of survivors, meanwhile, the obese group was the only category which mortality exceeded survival.

Slide 7

Include:

Neutrophil and platelet recovery time


  • No clear connection between time for neutrophil or platelet recovery and survival time
  • Interpretation should be aware of few data points and influence of outliers

HLA matching

Slide 10

Include: - Discussion

  • Conclusion

  • perspectivation?